CA1341100C - Determined dna sequences derived from a papilloma virus genome, their uses for in vitro diagnostic purposes and the production of antigenic compositions - Google Patents

Abstract

The invention concerns DNA fragments derived from the genomic DNA of HPV-33. These fragements are selected from the group of fragments extending between the nucleotide extremities defined hereafter in relation to tree nucleotide-numbering in figs. 1a and 1b respectively : 76 - 556, 543 - 864, 867 - 2811, 2728 - 3808, 3326 - 3575, 3842 - 4079, 4198 - 5611, 5516 - 7091. The invention also relates to the use of these fragments as probes for the detection of HPV in tissue cultures.

Description

'341100 DETERMINEp DNA SEQUENCES DERIVED FROM A PAPILLOMAVIRU~
GENQME. THEIR USES FOR IN VITRO DIAGNOSTIC PURPOSES AND
THE PRODUCTION OF ANTIGENIC COMPOSITIONS
The invention pertains to determined DNA sequences derived from a papillomavirus genome, more particularly DNA recombinants, including vectors, modified by such DNA
sequences in such manner that, when said DNA recombinants are introduced in suitable host cells in which said DNA
0 recombinants can be replicated, the said DNA sequences can be expressed in the form of the corresponding proteins.
The invention further relates to the proteins themselves, which can be purified and used for the production of immu-nogenic compositions.
The invention pertains more particularly to DNA
products of the papillomavirus designated as IP-2 (now re-designated as HPV-33) in the European patent application published under number 0192001 on August 27, 1986. A
plasmid containing the DNA o:E said virus has been deposit-ed at the CNCP~i ("Collection rationale de Culture de PZicro-Organismes" oz the Pasteur Institute of Paris) under number I-450.
Papil:lomaviruses are members of the papovavirus family and possess a genome of about 7,800 base pairs (bp) consisting oiE a covalently closed circular DNA molecule.
Human papilloma viruses (HPV) are classified on the basis of their DNA sequence homology (6) and nearly 40 types have now been described. Considerable insight into HPV
biology and their involvement in human disease has been attained by the application of the techniques of molecular biology. A possible role for HPVs in human cancer was suspected following the detection of HPV DNA in tumors resulting from the malignant conversion of genital warts (33). The cloning of two HPV genomes, HPV-16 and HPV-18 (3, 11) from cervical carcinomas has further stimulated research in this field of immense socio-economic impor-tance. These viruses were discovered in more than 70 ~ of the malignant genital tumors examined and in many others HPV-16 related sequences were detected (3, 16, 33).
Amongst these is HPV-33 which was recently cloned from an invasive cervical carcinoma using HPV-16 as a probe under conditions of reduced stringency (1). In the present study we have determined the DNA sequence of HPV-33 and describe its relationship to HPV-16. Among the papillomaviruses HPV-33 is unique as it possesses a 78 by tandem repeat which strongly resembles the enhancer of SV40 (4, 14).
The invention stems from the cloning strategy dis closed herea:Eter of the genome of HPV-33 which enabled particular D1!IA sequences to be identified, more particu larly those providing hybridization probes, particularly useful for ithe detection of DNA of papillomaviruses related to HPV-33 in human tissue, whereby positive responses can be related to the possible development in the host of invasive cervical carcinomas.
Reference is hereafter made to the drawings in which the figs concern respectively .
FIGS.Ia and lb.Nucleotide sequence of HPV-33. Position 1 on the circular genome corresponds to a "~-like"
sequence found by alignment with HPV-6b.
FIG. 2. Distribution of the major reading frames in the HPV-33 genome~. the reading frames were identified by comparison with other HPV sequences and the stop codons are represdented as vertical bars. Also indicated are the locations of unique restriction sites (S, ~I; E, ~qRV;
B2, ~g,~,II; H~1 , ~I ) and the likely polyadenylation signals (PA) for the early and late transcripts. In addition to these, 6 other potential PA sites (AATAAA) were detected at positions 862, 1215, 1221, 2666, 5837 and 6239.

FIG. 3. Principle features of the non-coding region. A
section of the non-coding region from positions 7500 to 114 is shown. The 78 by tandem repeats are overlined and those regions resembling the Z-DNA forming element of the SV-40 enhancer are indicated. Potential promoter elements are denoted by stars and the 3 copies of the 12 by palindrome enclosed between two rows of dots.
Preferred sequences are those which encode full proteins, more particularly and respectively the nucleo tidic sequences having the open reading frames referred to in table I hereafter.
The conditions under which the DNA sequence analysis were performed are defined under the heading "MATERIALS AND METHODS' hereafter. The conclusions which were drawn i:rom this sequence analysis appear under the heading "DISCIJSSION" .
MATERIALS AND METHODS
DNA secxuence analysis. The source of HPV-33 sequenced in this study was plasmid p15-5 (1) which consists of a III
linearized HF>V-33 genome cloned in a pBR322 derivative. A
library of random DNA fragments (400-800 bp) was prepared in M13mp8 (117) after sonication and end-repair of p15-5, essentially as described previously (28). DNA sequencing was performed by the dideoxy chain termination method (19, 20) with they modifications of Biggin et al. (2). Most of the seQuence was derived in this way although part of the non-coding region was found to be absent or underrepre-sented in they M13 library (> 300 clones). The sequence of this region ways obtained directly from p15-5 using the me-thod of Smith (24). Briefly, restriction fragments isola-ted from 2 "complemenary" M13 clones were used to prime DNA synthesis. on templates prepared from p15-5 which had been linearize:d with a restriction enzyme and then treated with exonuclea.se III (200 units/pmol DNA for 1 h at 22'C).
Computer ana.lvsis. DNA sequences were compiled and analysed with the programs of Staden (26, 27) as modified by B. Caudron. Optimal alignments of DNA or protein sequences were obtained using the algorithm developed by Wilbur and Lipman (31).
RESULTS AND DISCUSSION
Genomic Arrartcrement of HPV-33 - The complete 7909 nucleo-tide sequences of HPV-33, determined by the M13 shotgun cloning/dideo~;y sequencing approach, is presented in Fig.
1. On average each position was sequenced 6.5 times. In agreement with the convention for other papillomavirus sequences the numbering begins at a site resembling the recognition sequence for j~I in the non-coding region.
An analysis of the distribution of nonsense codons (Fig. 2) shows that, as in all other sequenced papilloma viruses, the 8 major open reading frames are located on the same strand. Some features common to HPV-33 and HPV
types 1a, 6b and 16 together with the cottontail rabbit papillomavirus and the prototype bovine papillomavirus, BPV-1, (5, 7, 8, 13, 21, 22) include the overlap between the largest open reading frames in the early region, E1 and E2, and the inclusion of E4 within the section enco-ding E2. Interestingly, the III site used in the mole-cular cloning of HPV-33 is situated within the E1/E2 overlap. Another property common to all papillomaviruses, except BPV-1, is the overlap between the L1 and L2 reading frames. Following L1 is the 892 by non-coding region which, by analogy with HPV1 (15, 29) undoubtedly contains the origin of: replication and various transcriptional regulatory elements. The principal characteristics of the HPV-33 genome a:re summarized in Table 1.
~lucleot~ de Secru~ce Compari son with HPV-1~ - HPV-16 is the only other onc~ogenic papillomavirus, isolated from tumors of the ano-genital region, which has been completely se-quenced (22). The gross features of HPV-33 resemble those of HPV-16 except that the E1 reading frame of the latter . 5 1341100 is interrupi~ed. All of the coding sequences in HPV-33, except that of E5, are slightly shorter than their counterparts in HPV-16. This may contribute to the fact that its non--coding region, between L1 and E6 (Fig. 2), is 76 by longer thereby keeping the genomes nearly constant in size.
When the open reading frames were compared pair-wise (Table 2) it was found that E1, E2, E6, E7, L1 and L2 displayed between 65-75 % homology whereas those for E4 and E5 were more divergent (about 50 % homology). These findings confirm the heteroduplex analysis performed pre-viously (1). A comparative study (8) of papillomavirus E1 gene products showed that the polypetide consists of an NH2-terminal segment whose sequence is highly variable, and a COOH-terminal domain of well-conserved primary structure. The longest stretch of perfect sequence homo-logy, 33 nucleotides (positions 1275-1307, Fig. 1) is found near the 5'-end of the E1 reading frame in a region encoding the variable domain of the polypeptide. Several other regions of complete identity (19-28 nucleotides) were detected elsewhere in E1, and also in E2, L2 and L1.
As many of these sequences are not found in the genomes of other HPVs, such as HPV-1a and HPV-6b, this raises the possibility that the corresponding oligonucleotides could be produced and used as diagnostic hybridization probes for screening biopsy material from potentially tumorigenic lesions.
Potential Gene Products - The papillomavirus gene products may be divided into those which are believed to play a pu rely structural role, L1 and L2, and those required for viral propagation and persistence. The results of a compa-rison of the probable products of the major reading frames from HPVs-33, 16 and 6b are summarized in Table 2. As ex-pected there is strong identity between the ocogenic HPVs-33 and '16, particularly for the proposed E1, E6, E7, s 1341100 L2 and L1 proteins. When conservative substitutions are included the homology between the two L1 polypeptides increases to 90 1w suggesting that the corresponding capsids mush be antigenically related. In contrast, significantly weaker homologies were detected when the analysis was extended to include the benign genital wart-forming HPV-6b (Table 2). Comparison of the HPV-16 proteins with those of HPV-6b revealed slightly more homology than was found with HPV-33 suggesting a closer evolutionary relationship.
The non-cc~ina Region - The non-coding region of HPV-33 displays several unique properties and bears only weak resemblance t:o its homologue in HPV-16. Located between the L1 stop codon and including the putative polyadeny-lation signal for the late transcripts is a stretch of 223 by (position~c 7097-7320, Fig. 1) unusually rich in T + G
(79 t). Contained within this segment are two copies of a 19 by direct: repeat (with one mismatch) and 7 copies of the motif TTGTRTR (where R is A or G). The latter is also found 7 times in the corresponding region of HPV-i6 suggesting that it may represent a recognition site for proteins involved in replication. It should be noted that nascent replication forks have been localised in this regiion of the HPV-1 genome (29) and that the origin of replication of the Epstein-Barr virus consists of a family of repeated sequences (32).
A 12 by palindrome (ACCG....CGGT) that occurs ex clusively in the non-coding region of all papillomavirus genomes examined was recently reported.
Three copies were found in the HPV-33 genome (Fig. 3) and these occupy the same positions in the non-coding region of HPV-16. A role for the palindrome as a possible control site for the early promoter was proposed (4, 15) and indirect support is provided by our finding that the non-coding regions of HPVs, such as HPV-33, do not display the clustered arrangement of recognition sites for the promoter-specific, activation factor Sp1(12). This is in direct contrast to the situation in another papova virus, SV40 (12, 14).
The most striking feature of HPV-33 is a perfect 78 by tandem. repeat located 200 by after the putative origin of replication (Fig. 3). No other repeats of this size or sequence have been described in the genomes of other papillomaviruses. The presumed early promoter for HPV-33 is lo<:ated about 300 by downstream from the tandem repeat and the characteristic promoter elements (4) could be identified (Fig. 3). The size, position and arrangement of the 78 by repeats in the HPV-33 genome suggest that they may function as enhancers of viral transcription.
Tandem repeater of 72, 73 and 68 by have been located near the early promoter of SV40 (4, 14), in the LTR of moloney murine sarcomas virus (10), and in the BK virus genome (23) and shown to enhance transcription from PolII dependent promoters in a cis-active manner. From mutagenesis of the SV40 enhancer (14, 30) and sequence comparisons of charac-terized trans~criptional activators a consensus enhancer sequence was derived. This structure could not be detected in the 78 by repeat but a potential Z-DNA forming region was uncovered.. Z-DNA is believed to attract regulatory molecules to eukaryotic promoters and a Z-DNA antibody binding site has been demonstrated within the SV40 enhancex (18). The sequence to which this antibody binds is also found, albeit with a single mismatch, in the putative HPV-33 enhancer (positions 7520-7527, 7599-7606, Figs. 1, 3).
The proposed HPV-33 enhancer shows no extended sequence homology to the well-characterized enhancers nor to other papillomavirus regulatory regions. However, it has recently been demonstrated that an enhancer-like element is located in the non-coding region of BPV-1 and that it requires the E2 product for activation (25). These findings support our proposal that the 78 by tandem repeats could have enhancer function and may indicate that the relatively low homology (Table 2) between the E2 pro-teins of EIP'J-33 and 16 reflects a specificity for the corresponding enhancer/regulatory regions.
Table;s 1 and 2 which have been referred to in the instant disclosure follow.

3t 3~

TABLE 1. Principa.i features of the HPV-33 genome Open Reading START FIRST STOP
Frame ATG CODON mol.wt.

El 867 879 2811 TGA 72 387 E2 2728 2749 3808 TAA 40 20.7 a. Calculated from the first ATG where this exists or from the start of the open reading frame.

l0 1341100 TABLE 2. Comparison of HPV proteinsa HPVs Protein 33v16 33v6b 16v6b E6 65 (70) 36 (51) 37 E7 61(69) 55(60) 56 E1. , 61 (69) 50 (60) 53 E2 53 (65) 46 (58) 45 E4 52 (55) 39 (46) 48 E5 40(52) 39(43) 33 L2 64 (66) 52 (58) 53 L1 81 (75) 68 (69) 71 a - Expressed as % homology after alignment with the program of (31).Values in parenthesis represent % nucleotide sequence homology.

The invention relates more particularly to sequences corresponding to the open reading frames of E6, E7, E1, E2, E4, E5, L2, L1.
The invention pertains also the uses of these sequences as hybridization probes, either those which are useful also for the detection of other papillomaviruses, thus of groups of papillomaviruses - such as probes containing part or all of the open reading frames corres-ponding to L1 - or those which are more virus - specific, i.e. probes containing part or all of the open reading frame corresponding to.
It also relates to other probes which detect sub-groups of papillomaviruses, particularly probes for the detection of viruses which can be related to major classes of diseases, i.e. viruses associated with tumors.
By way of exaaaple of one of said probes one should mention that which contains the sequence positionned between nucleotides 1275 and 1307 according to the numbering of the nucleotides in figs. 1A, 1B.
Needless to say that the invention also pertains to all of said DNA sequences, when labelled by a suitable label, i.e. a radioactive enzymatic or immunofluorescent label.
DNAs derived from the viral genome and which carry nucleotides modified by a chemical group which can be recognized by antibodies also form part of the invention.
It is well known that such DNAs can be produced by nick-translation in the presence of nucleotides modified accordingly. These DNAs form particularly valuables hybri-dization probes which, when hybridized to a DNA prepara-tion containing the complementary strand sought, can be detected by the above mentioned antibodies.
The invention also pertains to the diagnostic methods per se. Suitable methods are examplified hereafter.
Several hybridization methods may be used. For example, the spot hybridization method includes, after ~2 1341100 denaturation of the DNA, the deposition of an aliquot of the DNA onto film supports (nitrocellulose or Gene-screenplus), the hybridization of each film under the usual conditions with the probe, and the detection of the radioactive hybrid by contact exposition of the hybridized film onto radiographic film. Another possibility is replicated culture hyridization which involves agarose gel electrophoresis separation of the DNA fragments resulting 0 from treatment of the DNA by restriction enzymes, the transfer of the fragments after alkaline denaturation onto films (nitrocellulose or Genescreenplus) and their hybridization under usual conditions with different mixtures of probes. The formation of radioactive hybrids ~5 is detected again by contact exposition of the hybridization support films onto radiographic film.
For :instance the probes of the invention can be used for the. detection of the relevant viruses (or DNAs thereof) in preparation consisting of a biopsy of cells 20 obtained by scraping a lesion, or of biopsy sections fixed with Carnoy':> mixture (ethanol, chloroform, acetic acid 6: 3: 1 ) and included in paraffin.
The above nucleotide sequences can be inserted in vectors, to provide modified vectors which, when intro 25 duced in the suitable cell host, are capable of providing for the transcription and, where appropriate, translation of said DNA. sequences to produce the corresponding proteins which. can then be isolated from cellular extracts of the hosts. Obviously it is within the knowledge of the 30 man skilled in the art to select the appropriate vectors, particularly in relation to the host to be transformed therewith. Vectors consist for instance of plasmids or phages which will be selected according to their reco-gnized capability of replicating in the corresponding 35 procaryotic cells (or yeast cells) and of allowing for the expression of the DNA sequence which they carry.
The invention also relates to DNA recombinants . . _ ,3 13 ~ 1 1 0 0 containing an insert consisting of a DNA sequence corres-ponding to any of the above-defined open reading frames or of a part thereof, and suitably engineered to allow for the expression of the insert in eucaryotic cells, parti-cularly cells of warm-blooded animal. Suitable DNA recom-binants are genetic constructs in which said insert has been placed under the control of a viral or eucaryotic promoter recognized by the polymerases of the selected cells and which further comprise suitable polyadenylation sites downstream of said insert.
By way of example, the invention pertains to DNA
recombinants containing any of the above-mentioned open-reading inserts placed under the control of a ~ 15 promoter derived from the genome of the SV40 virus. Such DNA recombinants - or vectors - can be used for the transformation of higher eucaryotic cells, particularly cells of mammals (for instance Vero cells). The invention further pertains to portions of the above identified DNA
sequences which, when inserted in similar vectors, are able to codes for portions of the corresponding proteins which have immunological properties similar to those encoded by the full nucleotide sequences mentioned above.
The similarity of immunological properties can be recognized by the capacity of the corresponding polypep-tides producE~d by the relevant host to be recognized by antibodies previously formed against the proteins produced by the cells previously transformed with vectors contain-ing the above mentioned entire DNA sequences.
It goes without saying that the invention also pertains to any nucleotidic sequence related to the pre-ceding ones which may be obtained at least in part synthetically, and in which the nucleotides may vary within the constrainsts of the genetic code, to the extent where these variations do not entail a substantial modifi-cation of the polypeptidic sequences encoded by the so-modified nucleotidic sequences.

~4 131100 It already flows from the preceding discussion that the invention also pertains to the purified proteins or polypeptides themselves as obtainable by the methods discussed hereabove. These polypeptides, when produced in a suitable host, can either be obtained from the cells, far instance after rupturing of their cell walls, or from the culture medium of said cells when excreted in said cell medium, depending on the cell DNA recombinant system which is used. The polypeptide obtained can then be purified by resorting to usual purification procedures. It should be understood that "purified" in the instant context means a level of purity such that, when electro-phoresed in SI)S-PAGE, the purified proteins yield a single detectable band, say by Western blot.
~5 The viral proteins obtained, more particularly the structural proteins, for :instance as a result of the expression o:E said DNA sequences in ~ coli, can be used for the ~n vitro detection of antibodies against papillo-mavirus likely to be detected in tissue samples of 20 patients possibly infected with papillomavirus.
Of ps~rticular relevance are the genetically engi-neered proteins having the peptidic sequences which can be deduced from the L1 and L2 open reading frames. Another peptide of interest is the E6 protein (E6 star), the 25 synthesis of which can be induced by splicing and which encoded by a nucleotidic sequence located between nucleo-tides 229 (donor site) and 404 (acceptor site) of the HPV
33 sequence (see more particularly Fig. 1A), which sites also define the putative splicing sites in the E6 open 30 reading frame of HPV 33. Reference may be had to the publication of Schneider-Gardicke and Schwartz, Embo. J., _5, 2285-2292, as concerns the conditions of the production of such proteins.
These purified polypeptides can in turn be used 35 for the production of corresponding antibodies which can ~3~1100 be used for diagnosing ~ vitro the presence of viral polypeptides in a biological fluid, particularly in a serum or tissue culture of a patient. Like in the prece-ding instance, the invention relates to portions of the 5 above defined polypeptides, particularly those which are recognized by the same antibodies or to the contrary are able to elicit i~ vivo the production of antibodies recognizing the complete proteins.
It must be understood that the inventions relates 10 also specifically to the particular peptides encoded by the DNA regions specifically referred to in the preceding disclosure .and which have been found of particular interest.
The invention further concerns host cells trans 15 formed with DNA recombinants containing nucleotidic sequences directing the expression of the different peptides mentioned hereabove, and effectively capable to produce said peptides when cultured in an appropriate culture medium.
The invention finally also pertains more particu-larly to the antibodies themselves which can be obtained from an animal, such as rabbit, immunized in standard manner with said purified polypeptides and/or from hybri-domas previously prepared also in any known manner. Of particular inerest are the antibodies (polyclonal and monoclonal antibodies) directed against the strutural proteins. These antibodies are useful for the detection of viral infection. The antibodies which recognize the L1, L2 and E6 proteins of HPV-33 are of particular significance. Antibodies specific of L2 provide diagnostic tools for the 'fin vitro detection of specific viruses sharing with HPV-33 a sequence encoding a similar L2 protein. Antibodies specific to L1 are useful for the detection of the groups of viruses, to which HPV-33 x belongs. Antibodies specific to the E6 protein are useful for the detection of the oncogenic character of the virus causing the ahovesaid viral infection.
The invention also relates to intergenic sequences of particular interest, particular the 78 by sequence.
This sequence' is of part:icular interest as a possible insert in eucaryotic vectors, particularly in a position upstream of the promoter and downstream of the site at which transcription of the gene or nucleotide sequence the transcription of which is sought is initiated in the relevant host.
Particularly these documents can be referred to as concerns the definition of expressions used in this appli-cation where <~.ppropriate. As such they form part of the present disclosure.

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Claims (9)

1. A nucleic acid characteristic of oncogenic papillomaviruses, wherein said nucleic acid comprises the sequence of a human papillomavirus HPV-33 genomic DNA region selected from:
a) a region specific to HPV-33 and not found in the genome of HPV-16, HPV-1a and HPV-6b, or b) a region of HPV-33 showing complete identify with a region of HPV-16 genome, and not found in the genome of HPV-1a and HPV-6b.

2. The nucleic acid of claim 1, wherein said nucleic acid comprises the sequences of the perfect 78 bp tandem repeat represented in figure 3.

3. The nucleic acid of claim 1, wherein said nucleic acid comprises the sequence of the region between nucleotide positions 1275 to 1307 of Figure 1.

4. The nucleic acid of claim 1, wherein said nucleic acid comprises the sequence of a 19-28 nucleotides long region of complete identity between genomes of HPV-33 and HPV-16, said region absent from the genomes of HPV-1a and HPV-6b.

5. The nucleic acid of any one of claims 1 to 4, wherein said nucleic acid is a probe, more preferably an oligonucleotide probe.

6. A method of detecting the presence of an oncogenic papillomavirus in a sample, which comprises the steps of:
a) contacting the probe defined in anyone of claims 1 to 5 with nucleic acids of said sample; and b) detecting the formation of a hybridization complex as an indication of the presence of said oncogenic papillomavirus.

7. A method of detecting a tumorigenic lesion caused by a papillomavirus in as biopsy material which comprises the steps of:

a) contacting the probe defined in anyone of claims 1 to 5, with the nucleic acids of said biopsy material, and b) detecting the formation of a hybridization complex as an indication of the presence of said tumorigenic lesion and of its causative agent.

8. The use of a probe as defined in anyone of claims 1 to 5 for detecting an oncogenic papillomavirus.

9. The use of a probe as defined in anyone of claims 1 to 5, for the detection of the presence of a tumorigenic lesion caused by said papillomavirus.